LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 50.0% methanol mole fraction solution
# with 2500 methanol molecules in implicit water.
#
#
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
#
# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)


# Initialize simulation box
dimension       3
boundary        p p p
units           real
atom_style      molecular

# Set potential styles
pair_style      hybrid/overlay table spline 500 local/density

# Read molecule data and set initial velocities
read_data       methanol_implicit_water.data
Reading data file ...
  orthogonal box = (-31.123000 -31.123000 -31.123000) to (31.123000 31.123000 31.123000)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2500 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.005 seconds
velocity        all create  3.0000e+02 12142 rot yes dist gaussian

# Assign potentials
pair_coeff          1     1 table         methanol_implicit_water.pair.table PairMM
WARNING: 93 of 500 force values in table PairMM are inconsistent with -dE/dr.
WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 254 of 500 distance values in table 1e-06 with relative error
WARNING:  over PairMM to re-computed values (src/pair_table.cpp:473)
pair_coeff          *     * local/density methanol_implicit_water.localdensity.table




#Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box

#Thermostat & time integration
timestep        1.0
thermo          100
thermo_style    custom etotal ke pe temp evdwl

#minimization
minimize        1.e-4 0.0 1000 1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair_style  local/density  command:

@Article{Sanyal16,
 author =  {T.Sanyal and M.Scott Shell},
 title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
 journal = {J.~Chem.~Phys.},
 year =    2016,
 DOI = doi.org/10.1063/1.4958629}

@Article{Sanyal18,
 author =  {T.Sanyal and M.Scott Shell},
 title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
 journal = {J.~Phys.~Chem. B},
 year =    2018,
 DOI = doi.org/10.1021/acs.jpcb.7b12446}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 17
  ghost atom cutoff = 17
  binsize = 8.5, bins = 8 8 8
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair table, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) pair local/density, perpetual, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 7.855 | 7.855 | 7.855 Mbytes
TotEng KinEng PotEng Temp E_vdwl 
   1283.8556    2234.7133   -950.85771          300   -950.85771 
  -10.187232    2234.7133   -2244.9005          300   -2244.9005 
   -124.3661    2234.7133   -2359.0794          300   -2359.0794 
   -146.7158    2234.7133   -2381.4291          300   -2381.4291 
Loop time of 0.528503 on 4 procs for 244 steps with 2500 atoms

99.7% CPU use with 4 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
     -950.857712502527   -2381.2294195605  -2381.42909821383
  Force two-norm initial, final = 135.25170 2.3117934
  Force max component initial, final = 14.083102 0.60833889
  Final line search alpha, max atom move = 0.18347073 0.11161238
  Iterations, force evaluations = 244 278

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.48518    | 0.48843    | 0.49223    |   0.4 | 92.42
Bond    | 1.0084e-05 | 1.0861e-05 | 1.1483e-05 |   0.0 |  0.00
Neigh   | 0.018199   | 0.019153   | 0.020036   |   0.5 |  3.62
Comm    | 0.010229   | 0.014832   | 0.018994   |   2.6 |  2.81
Output  | 3.7985e-05 | 4.2069e-05 | 5.3874e-05 |   0.0 |  0.01
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.006032   |            |       |  1.14

Nlocal:        625.000 ave         638 max         618 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Nghost:        3613.75 ave        3640 max        3580 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs:        66411.2 ave       70713 max       62416 min
Histogram: 1 0 1 0 0 0 1 0 0 1

Total # of neighbors = 265645
Ave neighs/atom = 106.25800
Ave special neighs/atom = 0.0000000
Neighbor list builds = 13
Dangerous builds = 0

#set up integration parameters
fix             timeintegration all nve
fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 59915

#Equilibration (for realistic results, run for 2000000  steps)
reset_timestep  0
thermo          200
thermo_style    custom etotal ke pe temp evdwl

#run equilibration
run             2000
  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 6.730 | 6.730 | 6.731 Mbytes
TotEng KinEng PotEng Temp E_vdwl 
   -146.7158    2234.7133   -2381.4291          300   -2381.4291 
   540.68168      2041.44   -1500.7584    274.05395   -1500.7584 
    945.4949    2163.7509    -1218.256    290.47363    -1218.256 
   1118.7729    2195.7579    -1076.985    294.77042    -1076.985 
   1215.0058    2233.2445   -1018.2387    299.80282   -1018.2387 
   1251.8045    2240.8439   -989.03944      300.823   -989.03944 
    1206.649    2149.5807   -942.93169    288.57134   -942.93169 
   1290.6111    2248.3623   -957.75117    301.83231   -957.75117 
   1312.8944     2219.147   -906.25264     297.9103   -906.25264 
    1260.002    2211.4176   -951.41561    296.87266   -951.41561 
   1335.0956    2270.1367   -935.04108    304.75543   -935.04108 
Loop time of 3.56721 on 4 procs for 2000 steps with 2500 atoms

Performance: 48.441 ns/day, 0.495 hours/ns, 560.663 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.3122     | 3.3399     | 3.3633     |   1.0 | 93.63
Bond    | 7.5941e-05 | 8.062e-05  | 8.7627e-05 |   0.0 |  0.00
Neigh   | 0.03524    | 0.036666   | 0.037864   |   0.6 |  1.03
Comm    | 0.080116   | 0.10444    | 0.13373    |   6.1 |  2.93
Output  | 0.00019977 | 0.00022502 | 0.00029007 |   0.0 |  0.01
Modify  | 0.077781   | 0.078206   | 0.078752   |   0.1 |  2.19
Other   |            | 0.007641   |            |       |  0.21

Nlocal:        625.000 ave         637 max         616 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost:        3597.25 ave        3610 max        3586 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs:        66468.2 ave       69230 max       62721 min
Histogram: 1 0 0 1 0 0 0 0 0 2

Total # of neighbors = 265873
Ave neighs/atom = 106.34920
Ave special neighs/atom = 0.0000000
Neighbor list builds = 20
Dangerous builds = 0

#turn off recentering during production run
unfix recentering


#setup trajectory output
dump            myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
dump_modify     myDump element M
dump_modify     myDump sort id

#run production (for realistic results, run for 10000000 steps)
reset_timestep  0
thermo          1000
thermo_style    custom etotal ke pe temp  evdwl
run             10000
  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.071 | 8.071 | 8.071 Mbytes
TotEng KinEng PotEng Temp E_vdwl 
   1335.0956    2270.1367   -935.04108    304.75543   -935.04108 
   1266.2305    2227.2123   -960.98186    298.99303   -960.98186 
   1304.2289    2238.1343   -933.90544    300.45925   -933.90544 
   1311.3201    2232.0862    -920.7661    299.64733    -920.7661 
   1289.9028    2241.3533   -951.45049    300.89139   -951.45049 
   1314.2234    2244.8514   -930.62797      301.361   -930.62797 
   1282.2744    2240.6716   -958.39719    300.79987   -958.39719 
    1239.302    2181.5711    -942.2691    292.86591    -942.2691 
   1327.0954    2242.6441   -915.54875    301.06468   -915.54875 
   1334.9799    2239.6841   -904.70423    300.66731   -904.70423 
   1320.6105    2263.4912   -942.88066     303.8633   -942.88066 
Loop time of 23.3399 on 4 procs for 10000 steps with 2500 atoms

Performance: 37.018 ns/day, 0.648 hours/ns, 428.451 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 21.343     | 21.606     | 21.766     |   3.7 | 92.57
Bond    | 0.00045963 | 0.0004817  | 0.0005083  |   0.0 |  0.00
Neigh   | 0.20708    | 0.22081    | 0.22733    |   1.7 |  0.95
Comm    | 0.63014    | 0.80326    | 1.0801     |  19.8 |  3.44
Output  | 0.11791    | 0.14443    | 0.22211    |  11.8 |  0.62
Modify  | 0.37291    | 0.389      | 0.41719    |   2.7 |  1.67
Other   |            | 0.1761     |            |       |  0.75

Nlocal:        625.000 ave         636 max         613 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost:        3597.00 ave        3613 max        3580 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs:        66408.5 ave       69186 max       61728 min
Histogram: 1 0 0 0 0 0 1 0 1 1

Total # of neighbors = 265634
Ave neighs/atom = 106.25360
Ave special neighs/atom = 0.0000000
Neighbor list builds = 102
Dangerous builds = 0


Total wall time: 0:00:27
